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Property Graphs for Open Biological Ontologies

Property Graphs library for Open Biological and Biomedical Ontologies (OBO) in Python. This library supports reading OBO formatted ontologies into python data structures. It also supports generation of cypher statements to load the ontology into a property graph database like RedisGraph.

Installing

You can install the package via:

pip install pygobo

Using the command-line interface

The module can be invoked directly and provides a set of basic commands that allow parsing, inspection, cypher statement generation, and loading ontologies.

The invocation is:

python -m pygobo {operation} {file ...}?

where operation is one of:

  • parse - parse the ontology syntax
  • cypher - generate cypher create/merge statements
  • load - load the ontology into a property graph database
  • structure - output the general structure of the ontology

The operations can be scoped via the --scope option that takes the values:

  • all - all the components
  • ontology - only the top-level ontology metadata
  • term - only the ontology terms
  • xref - only the cross references
  • typedef - only the type definitions.

The scope option can be used multiple times to display different items.

If the file is omitted, the command will read from stdin. Otherwise, each file specified will be read and operated on in the order they are specified.

Loading ontology property graphs

The module currently supports loading ontologies directly into RedisGraph.

The following options can be specified for connecting to the database:

  • --host {name}|{ip} - the host of the database, defaults to 0.0.0.0
  • --port {port} - the port, defaults to 6379
  • --password {password} - the database password, default is no password
  • --graph {key} - the graph key, defaults to "obo"

Adding the --show-query option will allow you to see the Cypher statements as they are executed.

The --scope option will limit the loading to a specific aspect of the ontology but the order is presumed to be: ontology, term, xref, typedef. If you violate this ordering, the cypher statements may fail.

Formats Supported

The library only currently supprts the OBO formatted ontologies. That is, it can't currently load the OWL/XML format.

You can convert OWL/XML formatted ontologies into OBO format using the robot tool.

API

OBOParser

An ontology can be easily loaded from a stream source:

from pygobo import OBOParser
parser = OBOParser()
with open('ontology.obo','r') as input:
   ontology = parser.parse(input)

Ontology

An ontology is a simple class with the following fields:

  • metadata - a dictionary of ontology metadata
  • terms - a dictionary of ontology terms
  • typedefs - a dictionary of ontology type definitions

Some property values are structured dictionaries, some are tuples, and some are simple values.

Generating Cypher

Once an ontology is loaded, the query_generate function can be used to generate cypher load statements. The usage is:

for query in query_generate(ontology,scope=['ontology']):
   print(query)
   print(';')

The scope keyword argument is a list of scope values. The values are the same as the command-line interface (see above).

Property graph structure

The graph is is documented in the schema (view, source).